Step 1: Prepare a simulation

Before running a simulation, you will need to define a force field. The SMOG resource provides two different approaches.

SMOG 2: SMOG 2 is a downloadable software package with which you can define almost any concievable structure-based model, for systems of arbitrary molecular composition, complexity, energetic representation (e.g. ions and electrostatics) and size. Also, SMOG 2 provides support for the OpenSMOG library, which allows all SMOG models to be simulated with OpenMM. A subset of models generated by SMOG 2 will be compatible with Gromacs, NAMD and LAMMPS.

SMOG Webtool: If you want to use the most basic forms of SMOG models, then the webtool is probably sufficient. Force fields generated with the webtool may be used in Gromacs, or unofficial modified versions of Gromacs. Some of the models may also be used with NAMD, OpenMM, or LAMMPS.

This resource is provided by the Center for Theoretical Biological Physics.
Please direct questions and comments to info@smog-server.org.
Page created and maintained by Jeff Noel and Paul Whitford